def test_x_affected_male_ref_call():
"""Test an affected ref call male"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t1\t2\n"
]
family = get_family(family_lines=family_lines)
homozygote_variant = {'genotypes': {}}
homozygote_variant['genotypes']['proband'] = Genotype(**{'GT': '0/0'})
assert check_X_dominant(variant=homozygote_variant, family=family) == False
def test_x_affected_recessive_male():
"""Test a sick male
"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t1\t2\n"
]
family = get_family(family_lines=family_lines)
recessive_variant = {'genotypes': {}}
recessive_variant['genotypes']['proband'] = Genotype(**{'GT': '0/1'})
assert check_X_dominant(variant=recessive_variant, family=family) == True
def test_x_healthy_homozygote_female():
"""Test an healthy homozygote female"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t2\t1\n"
]
family = get_family(family_lines=family_lines)
homozygote_variant = {'genotypes': {}}
homozygote_variant['genotypes']['proband'] = Genotype(**{'GT': '1/1'})
assert check_X_dominant(variant=homozygote_variant, family=family) == False
def test_x_affected_recessive_female():
"""Test a sick heterozygote female
Females needs to bo hom alt to follow pattern
"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t2\t2\n"
]
family = get_family(family_lines=family_lines)
recessive_variant = {'genotypes': {}}
recessive_variant['genotypes']['proband'] = Genotype(**{'GT': '0/1'})
assert check_X_dominant(variant=recessive_variant, family=family) == True
def test_x_affected_no_call_male():
"""Test a sick male with no gt call
This should be true since there is no information that contradicts the model
"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t1\t2\n"
]
family = get_family(family_lines=family_lines)
no_call_variant = {'genotypes': {}}
no_call_variant['genotypes']['proband'] = Genotype(**{'GT': './.'})
assert check_X_dominant(variant=no_call_variant, family=family) == True
def test_x_affected_male_ref_call():
"""Test an affected ref call male"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t1\t2\n"
]
family = get_family(family_lines=family_lines)
homozygote_variant = {'genotypes': {}}
homozygote_variant['genotypes']['proband'] = Genotype(**{'GT':'0/0'})
assert check_X_dominant(
variant = homozygote_variant,
family = family
) == False
def test_x_healthy_homozygote_female():
"""Test an healthy homozygote female"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t2\t1\n"
]
family = get_family(family_lines=family_lines)
homozygote_variant = {'genotypes': {}}
homozygote_variant['genotypes']['proband'] = Genotype(**{'GT':'1/1'})
assert check_X_dominant(
variant = homozygote_variant,
family = family
) == False
def test_x_affected_recessive_male():
"""Test a sick male
"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t1\t2\n"
]
family = get_family(family_lines=family_lines)
recessive_variant = {'genotypes': {}}
recessive_variant['genotypes']['proband'] = Genotype(**{'GT':'0/1'})
assert check_X_dominant(
variant = recessive_variant,
family = family
) == True
def test_x_affected_recessive_female():
"""Test a sick heterozygote female
Females needs to bo hom alt to follow pattern
"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t2\t2\n"
]
family = get_family(family_lines=family_lines)
recessive_variant = {'genotypes': {}}
recessive_variant['genotypes']['proband'] = Genotype(**{'GT':'0/1'})
assert check_X_dominant(
variant = recessive_variant,
family = family
) == True
def test_x_affected_no_call_male():
"""Test a sick male with no gt call
This should be true since there is no information that contradicts the model
"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t1\t2\n"
]
family = get_family(family_lines=family_lines)
no_call_variant = {'genotypes': {}}
no_call_variant['genotypes']['proband'] = Genotype(**{'GT':'./.'})
assert check_X_dominant(
variant = no_call_variant,
family = family
) == True
def test_x_affected_no_call_male_strict():
"""Test a sick male with no gt call
This should not be true since we allways need 'proof'
for an inheritance pattern if strict mode.
"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t1\t2\n"
]
family = get_family(family_lines=family_lines)
no_call_variant = {'genotypes': {}}
no_call_variant['genotypes']['proband'] = Genotype(**{'GT': './.'})
assert check_X_dominant(variant=no_call_variant,
family=family,
strict=True) == False
def test_x_affected_no_call_male_strict():
"""Test a sick male with no gt call
This should not be true since we allways need 'proof'
for an inheritance pattern if strict mode.
"""
family_lines = [
"#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
"1\tproband\t0\t0\t1\t2\n"
]
family = get_family(family_lines=family_lines)
no_call_variant = {'genotypes': {}}
no_call_variant['genotypes']['proband'] = Genotype(**{'GT':'./.'})
assert check_X_dominant(
variant = no_call_variant,
family = family,
strict = True
) == False